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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
REDItools Resource Report Resource Website 100+ mentions |
REDItools (RRID:SCR_012133) | software resource | A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. | standalone software, illumina, roche, pacific biosciences, life technologies, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:23742983 | MIT License | biotools:reditools, OMICS_05860 | https://bio.tools/reditools | SCR_012133 | 2026-09-19 12:52:25 | 152 | |||||||
|
PrimerProspector Resource Report Resource Website 10+ mentions |
PrimerProspector (RRID:SCR_012136) | software resource | A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21349862 | OMICS_05884 | SCR_012136 | 2026-09-19 12:52:25 | 26 | |||||||||
|
iceLogo Resource Report Resource Website 100+ mentions |
iceLogo (RRID:SCR_012137) | software resource | Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol. | standalone software, web app, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:19876014 | Apache License | biotools:icelogo, OMICS_05885 | https://bio.tools/icelogo | SCR_012137 | 2026-09-19 12:52:25 | 185 | |||||||
|
Musite Resource Report Resource Website 10+ mentions |
Musite (RRID:SCR_012141) | software resource | A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20702892 | OMICS_05941 | SCR_012141 | 2026-09-19 12:52:25 | 13 | |||||||||
|
AMS Resource Report Resource Website |
AMS (RRID:SCR_012140) | software resource | Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22555647 | Apache License | OMICS_05934, biotools:ams | https://bio.tools/ams | SCR_012140 | AutoMotif Service | 2026-09-19 12:52:25 | 0 | ||||||
|
PhosphoSiteAnalyzer Resource Report Resource Website |
PhosphoSiteAnalyzer (RRID:SCR_012142) | software resource | A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22471441 | Free, Public | biotools:phosphositeanalyzer, OMICS_05951 | https://bio.tools/phosphositeanalyzer | SCR_012142 | 2026-09-19 12:52:25 | 0 | |||||||
|
HLAforest Resource Report Resource Website 1+ mentions |
HLAforest (RRID:SCR_012146) | software resource | Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest. | standalone software, perl |
is listed by: OMICtools has parent organization: Google Code |
PMID:23840783 | Free for academic use, Apache License | OMICS_06170 | SCR_012146 | 2026-09-19 12:52:26 | 6 | ||||||||
|
DNAcopy Resource Report Resource Website 100+ mentions |
DNAcopy (RRID:SCR_012560) | DNAcopy | software resource | Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
OMICS_00720, biotools:dnacopy | https://bio.tools/dnacopy, https://sources.debian.org/src/r-bioc-dnacopy/ | SCR_012560 | 2026-09-19 12:52:30 | 349 | ||||||||
|
A sample size calculation method Resource Report Resource Website |
A sample size calculation method (RRID:SCR_009469) | A sample size calculation method | software resource | Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author. | is listed by: OMICtools | PMID:24314022 | OMICS_01228 | SCR_009469 | 2026-09-19 12:51:48 | 0 | |||||||||
|
NGC Resource Report Resource Website |
NGC (RRID:SCR_009342) | NGC | software resource | A compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files. | is listed by: OMICtools | PMID:23066097 | OMICS_00964 | SCR_009342 | 2026-09-19 12:51:48 | 0 | |||||||||
|
iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-09-19 12:51:49 | 11 | ||||||
|
Gecko Resource Report Resource Website 500+ mentions |
Gecko (RRID:SCR_009001) | Gecko | software resource | A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15588317 | OMICS_00758 | SCR_009001 | Gene Expression: Computation and Knowledge Organization, Geckoe | 2026-09-19 12:51:47 | 547 | ||||||||
|
Quip Resource Report Resource Website 50+ mentions |
Quip (RRID:SCR_009362) | Quip | software resource | Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats with extreme prejudice. | is listed by: OMICtools | OMICS_00965 | SCR_009362 | 2026-09-19 12:51:48 | 56 | ||||||||||
|
MFCompress Resource Report Resource Website 1+ mentions |
MFCompress (RRID:SCR_009301) | MFCompress | software resource | A compression tool for FASTA and multi-FASTA files. | is listed by: OMICtools | PMID:24132931 | OMICS_00963 | SCR_009301 | 2026-09-19 12:51:48 | 3 | |||||||||
|
RLZ Resource Report Resource Website |
RLZ (RRID:SCR_009420) | RLZ | software resource | Optimized relative Lempel-Ziv compression of genomes. | is listed by: OMICtools | OMICS_00966 | SCR_009420 | Relative Lempel-Ziv Compression of Genomes | 2026-09-19 12:51:48 | 0 | |||||||||
|
GReEn Resource Report Resource Website 100+ mentions |
GReEn (RRID:SCR_009264) | GReEn | software resource | A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Aveiro; Aveiro; Portugal |
PMID:23872967 PMID:22139935 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00959 | SCR_009264 | Genome Resequencing Encoding | 2026-09-19 12:51:48 | 346 | |||||||
|
SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data analysis software, data processing software, software application, software resource | Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells. | small RNAs datasets, ubiquitous miRNA modifications, human embryonic cells, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Health ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-09-19 12:51:50 | 31 | ||||||
|
ISRNA Resource Report Resource Website 1+ mentions |
ISRNA (RRID:SCR_009565) | ISRNA | software resource | An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | PMID:24300438 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00360 | SCR_009565 | Integrative Short Reads NAvigator | 2026-09-19 12:51:50 | 3 | |||||||
|
shortran Resource Report Resource Website |
shortran (RRID:SCR_009636) | shortran | software resource | A pipeline for small RNA-seq data analysis. | is listed by: OMICtools | PMID:22914220 | Free | OMICS_00368 | SCR_009636 | 2026-09-19 12:51:51 | 0 | ||||||||
|
SCALCE Resource Report Resource Website |
SCALCE (RRID:SCR_009658) | SCALCE | software resource | A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00969 | SCR_009658 | Boosting Sequence Compression Algorithms using Locally Consistent Encoding | 2026-09-19 12:51:51 | 0 |
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